I want my galaxies set up with 5-7 major empires. I want the other ~15 races to be largely limited to filling the galaxy with independent planets (which I have set to abundant). However, the independent planets only consist of those races that are major empires (I've checked in the editor). My various minor races only appear in the occasional colony ship, and never as pre-existing colonies. How do I fix this? Do I need to play around with the playable/expanding Y/N flags?

Are you sure the independents are only using races of existing empires? It could be all those you found just wound up as the same race of existing empires.

An easy way to test this would be to make a 1400 star galaxy, starting everything, 1 AI empire, teeming independents. Then go into the editor and see if there are any independent colonies which are a different race.

As for forcing the issue, I don't know of a way to determine which races show up as independents other than using the game editor.

EDIT: I just did 3 games with those settings plus no pirates (can hide colonies) and here's the results.

Looks like the number of independents is limited by how many empires there are. The first independent was always the same as my race, but the second is a new race. One thing to note is that the colonies seem to for in clumps, or have 1-2 within a sector of each other. Over 90% of the map was devoid of colonies.